Harry Potter and the Return of the Pharaoh
by Animefanguy
Summary: Summer after Third year, things are finally better for Harry Potter. But when our young hero discovers a puzzle in a box, abandoned by Dudley after his winter vacation to Egypt, things are about to get an unexpected turn and a lot of plans are about to shattered to pieces. M for safety reasons. Hiatus until 15/10/2018


**Hey everyone I'm back and with a new story to boot.**

 **Now I have been reading a few Yugioh+Harry Potter fanfictions and this particular idea popped into my head I hope you enjoy it.**

 **For those wondering for my other stories, there is another new one that is in the making before I go back to update the existing ones.**

 **If you find any grammatical error please go easy on me I do not have a Beta.**

 **Well anyway let's move on, but first:**

 **DISCLAMER: I DO NOT own Harry Potter or Yugioh, if I did well… a lot of things would have been different.**

 **NOW ON WITH THE SHOW.**

Harry was still smiling as he entered #4 privet Drive, with the 'threat' of his godfather being a 'ruthless murderer' that will keep taps on him hanging over the Dursleys head he will finally have a somewhat peaceful summer. Though he would have preferred to move in with Sirius he will take what he could get.

"Now boy" his uncle said as he closed the front door, Harry turned to face him. Vernon was trying to look as threatening as possible, but his fear of Harris godfather was still fresh on his mind so he failed to sound intimidating.

"Put your things in the cardboard under the stairs and make sure that that bird of yours stays in its cage, I will not have it flying around being spotted by the neighbors"

"But uncle you forget; my godfather wants constant updates that I'm all right, if he doesn't get them he will come and here in order to check for himself. You don't want him to come here do you?" Harry said the most innocent voice he could muster, inwardly laughing at his uncle's terrified face.

"F–fine… but your stuff go to the cardboard" Vernon demanded hoping to win at least a part of the argument. Harry just shook his head.

"Now uncle my godfather will want to know that I am safe and happy, and you taking away my things is something that will make me unhappy, you don't want me to contact him about it right?" Harry new that he had to milk this situation as much as possible as it was rare for him to have the upper hand.

Vernon's fat face was turning purple with rage, but he knew that if he hit the boy he will not survive his godfather. With a huff he started walking towards the kitchen.

As Harry started carrying his trunk up the stairs he stopped and observed the new photos that were hanging on the staircase walls. They showed his relatives smiling at the camera in a desert with the Egyptian pyramids behind them.

Harry heard steps from behind him; he turned arrowed and saw his aunt exiting the livingroom with a scowl appearing on her face after seeing him.

"When did you guys go to Egypt?" he asked with a raised eyebrow.

"During winter break" Petunia answered with her nose in the air. "And just so you know Ickle Dudleykins has put the thing he doesn't want in your bedroom" she said and left to go meat her husband in the kitchen.

Harry raised an eyebrow before closing his eyes and sighing, looks like he will be cleaning his room from Dudley's vacation junk, which would most definitely be worthless.

He finally reached the door to his room, opened it and entered. His room was almost exactly like he had left it, with the exception of the dust that had piled up and a small mountain of items in one of the corners of the room, Dudley's junk.

Releasing another sigh, Harry left his trunk and Hedwig's cage in the middle of the room; he opened the window to get some fresh air, and then opened the cage to let his familiar out, Hedwig few out of the room in order to stretch her wings.

Harry sat on his bed and looked around, his eyes fell on the junk pile and with a sigh he stood up and approached it in order to clear it up.

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After about an half an hour Harry was almost done with checking all the items in the pile and as he had predicted everything he had checked up until now was junk, things like a broken MP3 player, boxes and paper bags from purchases, a cracked sphinx model, and other things. He did find a couple of interesting things, like a scroll with hieroglyphics on it and an explorer's bag that was still in fairly good condition.

Just as he put aside a pair of broken binoculars his eyes landed on a peculiar site, there laying in front of him was a box that looked like it was made of gold, it had hieroglyphics all over its surface with a big eye symbol on two of its sides(the millennium puzzle box). Harry stared at it for a minute before picking it up; he knew it wasn't made of gold, the Dursleys could not afford such a thing, and even if they did they would not have thrown it in the pile of junk.

His curiosity picked Harry opened the box to find it filled with pieces made from the same gold like metal as the box. He got up and went to his desk and removed the strange pieces from the box. There were at least a few dozen of these pieces in front of him. He slowly picked up one of the largest pieces, the one with the eye and looked at it.

"This… this is a puzzle," he said to himself as he looked back at the pieces on his desk. Harry actually liked puzzle games, they intrigued him from the simplest like the mini Rubik's cube to the most intricate like a complex maze. He found them challenging, plus puzzle games were the only games he got as a child that were in almost perfect condition, seeing that Dudley gave up on them almost instantly thus allowing Harry to take then.

He looked at the clock hanging at the wall and saw that it was still early.

"Well why not?" Harry said with a smile. "I haven't solve a puzzle in years, this will be interesting," and with that he started trying to solve this intricate puzzle.

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A week has passed since Harry found this strange puzzle and some would say that he was becoming obsessed with solving it. With the exception of taking care of his needs (food, sleep, etc) and staying in contact with his friends; Harry spent most of his free time trying to solve the puzzle.

It was a strange feeling; there was something deep within himself that urged him to compete the puzzle. He wasn't sure what it was but it felt strangely familiar, like a memory that is at the back of your mind but you just can't remember it.

Lightning could be heard outside his closed window as black clouds covered the night sky and strong winds lashed on the trees, the storm was unexpected appearing out of nowhere about ten minutes ago. He had sent Hedwig with a letter to Hermione informing her about how he was doing.

Harry though wasn't paying attention at the weather, he was almost done, just two more pieces and the puzzle would be complete.

He took one of the remaining pieces and slid it in place; a week golden light appeared on the outline of the piece when it connected with other pieces, this phenomenon had happened every time Harry connected the correct pieces together. It indicated that perhaps the puzzle had some sort of magic, but in his desire to solve it, dismissed it as anything dangerous.

"I… I did it, just the last piece and the puzzle is finished" said Harry with happiness and anticipation in his voice; this was the hardest puzzle he had ever solved. Harry picked the last piece up and looked at it; it was the piece with the eye engraved on it.

"The last piece, here goes…" he said and slowly put it in its place. As the last piece clicked in place the pyramid like puzzle started to glow, Harry ignored the glow happy that he finished it and placed the puzzle around his neck.

The minute he placed it over his neck the light coming from the puzzle intensified, "What is going on?" asked Harry as the puzzle illuminated the room. Then his scar was assaulted by a piercing pain so great that made Harry scream, lightning and thunder roared from the heavens and the winds attacked everything with greater force then before, due to the storm no–one heard his screams. Nor did they hear a second scream; this one was a lot less human sounding like something out of a nightmare. Even though he was in incredible amount of pain, Harry realized that this second screaming voice was coming from his lightning–bolt scar.

Slowly from his scar a pitch black cloud started to emerge and as it did so a faint gold light started closing the scar, the origin of the second voice was following the cloud, and Harry though disoriented, due to the pain he was feeling, was able to follow the cloud with his eyes as it started to concentrated itself in a sphere of blackness in front of him.

As the last of the last of the cloud lest his scar and the light closed it completely, the pain Harry was feeling started to fade and he was able to now see clearly as the black sphere made out of smoke started to take a human shape.

As it finished shaping in the form of a man Harry froze, there in–front of him was a man with waxy–like reptilian pale white skin. The whites of his eyes had a blood-shot look and the eyes themselves were scarlet with cat-like slits for pupils. Harry knew who was standing before him.

"Voldemort…" Harry said while frozen in shock and fear. The ghost–like being chuckled, it was a chilling thing to hear.

"Yes, Harry Potter it is I Lord Voldemort, the most powerful sorcerer that has ever leaved… well I am a piece of him." He told the boy in front of him, the smirk on his face never leaving it.

"What?" Asked Harry, with a shocked expression on his face, what was he talking about.

"You see boy, when my body was destroyed all those years ago, a piece of my soul clutched itself on to you, specifically your scar" he said as he pointed at Harry's forehead, ignoring the fact that the scar was no longer there.

"That piece… that was you, wasn't it?" Harry asked while pointing at the apparition.

"Yes, after I entered your body I tried to take it over, but whatever that filthy mudblood mother of yours did stopped me, imprisoning me at the far reaches of your subconscious mind. But now that I am free, I SHALL BE TAKING OVER YOUR BODY HARRY POTTER!" Voldemort shouted as he launched himself at Harry.

But just as he was about to reach the boy, the puzzle around Harry's neck, more specifically the eye, started to release beams of light and a chime like sound was heard coming from it. Voldemort had to cover his eyes with his arm due to the blinding light.

Harry on the other hand felt enormous amounts of mystical energies enter his body, and then being guided by these energies, he uttered a phrase he had never heard or knew.

"Yu–Gi–Oh!"(1) the light from the puzzle intensified and covered him completely forcing the Dark Lord to take a step back.

As the light faded Voldemort lowered his hand and looked to were Harry was standing with his eyes closed, something had changed, the boy seamed taller, he was standing straighter than before. And then he saw it, at the boy's forehead he saw the eye of Anubis, not that he knew it was called that, glowing with a golden light. Harry slowly opened his eyes and what he saw made Voldemort pause, gone were the green eyes of the shy, insecure, frightened boy. In their place was a pair of emerald eyes that belonged to someone assertive, confident, determent.

Harry had never felt so good in his life! It was as if he regained a vital piece of himself even though he never knew it was missing. Opening his eyes he looked at Riddle and information started pouring from somewhere, he wasn't sure from where, but at the moment it did not mater.

"Tom Marvolo Riddle," Harry said in a commanding tone as he looked straight into Voldemort's eyes, for some reason Harry's voice sounded beeper.

"By my right as the holder of the Millennium Puzzle and my victory over your original self, I banish you to the Shadow Realm! Now begone!" He proclaimed with confidence, thrusting his right palm at Voldemort.

An incredible amount of pain went through the piece of Riddle's soul as he let out a scream, he felt like his very being was shattered into a million pieces, and then those pieces were banished from this dimension, trapped inside the Shadow Realm for all eternity.

As the soul piece disappeared and the eye of Anubis faded from his forehead, Harry lost consciousness and fainted on the ground.

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 **Thinis, Capital City of Magical Egypt, Palace of the Pharaoh**

In the bedchambers of one of the members of the Pharaoh's Sacred Court, a seventeen year–old woman shot up from her bed, sweat covering her face. Her name was Ishizu Ishtar, holder of the Millennium Necklace as of a month ago. Ishizu took a few deep breaths as she recalled the vision the Millennium Item had granted her.

She had seen the completion of the Millennium Puzzle; she had seen the event before, when she put on the Necklace for the first time, and her predecessor had seen the Puzzle's completion for more than ten years, but on those visions the face of the person who solved it was always shrouded in darkness.

This time it was different, she could not only see his face, she saw and heard his confrontation with a Dark Spirit. And now she knew the name of their new Pharaoh! Plus from the feeling she was getting from the Item her vision was of the present, the event that was revealed to her happened no more than five minutes ago!

The fact that the new Pharaoh was England's Boy–Who–Lived, or that Voldemort was the identity of the Dark Spirit was not lost to her. Harry Potter was celebrated as a Hero in the entire Magical World; the fact that he was destined to be their King will cause celebration amongst the masses.

Ishizu quickly got up, did her morning ritual and left to gather The Pharaoh's Sacred Court, even if it was still quite early they needed to be informed of the identity of the new King and device a plan in order to retrieve him.

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 **England, #4 Privet Drive**

Harry slowly started regaining consciousness as the warm rays of the sun started caressing his face, he looked around him while in confusion; he was lying in the middle of the floor, he slowly sat up as he tried to remember why he was lying on the floor. Then the events of last night came rushing back into the forefront of his mind.

Shock and disbelief washed over him as he slowly got to his feet; that actually happened? Did his scar really contain a piece of Voldemort's soul? And where did the knowledge to banish him come from? What was going on!?

As he looked around his room he noticed something else, "Am I… taller?" he asked in surprise as he looked at himself. Surprise appeared on his face as he checked himself, the muscles on his hands appeared more refined and the damage from his relatives starving him seemed to have disappeared.

More than that he felt incredible; his entire body was full of energy, like he could run for miles and not get tired, his mind was clearer then it had ever been before and thinking did not induce any sort of discomfort. But most importantly his magic felt like it had gained a tremendous boost, not only that but it seemed to be flowing through his body with extreme ease; if he had to compare it with how his magic felt previously, it would be like comparing a river of pure water with a river full of mud.

As he looked down he saw the puzzle hanging around his neck. "The Millennium Puzzle…" he said in a soft voice as he lifted it to the level of his eyes.

 _'_ _How do I know this thing's name?'_ he asked himself as he took a closer look. After a minute he sighed, releasing the Puzzle, and looked around the room again, his eyes landed on something that made him pause. _'Are those my glasses? But I can see perfectly.'_ He thought in disbelief as he touched his face instinctively reaching for the ones he should be wearing; his hand did not find any glasses.

"I… I can see" he said to himself, joy evident in his voice, he didn't need glasses anymore. Wishing to calm down Harry closed his eyes and took a few deep breaths. He decided to think about it after he had finished with his morning ritual, nodding to himself on his intended course of action he removed the Puzzle from his neck and headed towards the bathroom.

Once he entered the bathroom he removed his clothes and looked himself in the full body mirror that was hanging on one of the walls, his previous assumptions that he was taller and that the effects of malnutrition had disappeared were proven correct. His entire body had transformed into one that belonged to an Olympic swimmer, he slowly touched the six–pack that now adorned his stomach wanting to make sure he wasn't hallucinating.

As he took a closer look at his face he noticed that it seemed older more refined, plus his hair seemed to have gotten longer, as he brushed aside some of his hair he got his bigger shock yet; his scar was gone!

He quickly touched his forehead to make sure that he wasn't dreaming, as his hands felt the smooth skin of his forehead tears started falling from his eyes, he was free from that accursed symbol of his status as the blasted Boy–Who–Lived. Calming down he entered the bathtub to take a shower.

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After he got dressed and put the Millennium Puzzle over his neck Harry went downstairs in order to fix himself some breakfast. After he finished cooking a pair of fried eggs and some bacon, he filled a glass of orange juice he started eating. It was rather strange to not have to cook for his relatives, but the threat of Sirius coming over if they mistreated had caused the Dursleys to give him a lot of breathing room, no more chores, or getting shouted and beaten up. It was the best summer he ever had with his relatives.

Just as he finished cleaning the dishes his relatives entered the kitchen, not wanting to socialize with them Harry offered a good morning and started walking to the door. Unfortunately over the past week Dudley had been getting more and more frustrated over the fact he couldn't bully his cousin anymore, so when he saw the Puzzle he wanted to take it in order to get back at Harry for somehow making his parents forbid him to bully Harry.

"Hey what is that?" Dudley asked as he pointed at the Millennium Item, his parents looked at where their son was pointing and saw the Puzzle, both gaining curious looks.

"Oh this… well it's an item of 'my people'," said Harry while making air quotes.

"Well I want it!" said Dudley and reached out to take the Puzzle.

"No Dudley, don't!" shouted Harry as he tried to stop his fat cousin, unfortunately do to being surprised by the declaration he did not act fast enough and Dudley grabbed the Millennium Puzzle.

What happened next surprised Harry and terrified his aunt and uncle, the Puzzle started discharging electricity and shocking Dudley, he let out a pain filled scream as the Puzzle kept electrocuting him. Suddenly information pasted over Harry's mind about what to do in this situation.

"DUDLEY LET GO OF THE PUZZLE!" Harry shouted as he tried to pry his cousin's hand from the Item, after a few more seconds Dudley released the Puzzle and the electric discharge stopped. Harry wants as his cousin fell on the floor while twitching due to the electricity still in his body, his aunt rushed at her son's side while his uncle looks furiously at him.

"WHAT DID YOU DO TO MY SON YOU FREEK?" he shouted at Harry while his face became purple in anger, he forgot his fear of Sirius and raised his hand to strike him.

At that moment the Millennium Puzzle started glowing just as it did last night and the same chime was heard coming from it, again Harry, being guided by the mystical energies that entered his body once again said the same fraise as last time.

"Yu–Gi–Oh!" The transformation was near instant and he was ones again the Harry that had banished the Soul Piece of Voldemort to the Shadow Realm, the eye of Anubis shining proudly on his forehead. He narrowed his eyes as he saw his uncle's fist closing in.

"That's enough" said Harry with a commanding tone that froze his uncle in his tracks. Vernon was not sure what happened, but his nephew entire presence and stance changed. Even as a Muggle he could feel the power licking out of Harry, it made him uneasy.

Harry narrowed his eyes a bit and released a fraction of his power as pressure, he wasn't sure how he knew how to go that but he could.

Vernon took a step back as sweat started falling from his face, his instincts were screaming at him that the being in front of him was not prey, as he believed until now, but an apex predator, and he should not get in his way.

Harry turned his head a bit and looked at his aunt's eyes, as she looked at her nephew the rage that was raging inside of Petunia from seeing her precious sweetums hurt vanished, and in its place fear took hold.

"Now listen and listen carefully, I will no longer be punished for your son's mistakes; he just tried to take something that did not belong to him." He then turned his attention at his still twitching cousin.

"What he experienced was the defense mechanisms of the Puzzle, I tried to warn him but he ignored me. His current state is his own fault; I'm in no ways responsible are we clear?" he asked as he turned his attention back to the adults of the room.

Both his uncle and aunt nodded their heads in agreement, fear still evident on their face. Harry stared at them for a few seconds before he left the kitchen without another word.

As Harry closed the door to his room he felt most of the mystical energies that had entered his body leave; with the exception of a small piece that remained and bonded with his core, becoming a part of him. As the energies left the eye of Anubis disappeared from his forehead.

Harry took a deep breath and slowly exhaled trying to calm himself down; he moved to his bead and sat on it. What had happened was an incredible experience; he had never stood up to Vernon before in his life, the confidence he felt after he said that fraise was amazing.

He lifted the Puzzle at the level of his eyes and stared at it. This incredible item was the source of the change he was sure of it, and to be honest he liked the feeling of completion he got whenever he activated it.

With a sigh he let the Puzzle drop on his neck as he got up and walked to his window; he knew he had a lot of thinking to do, from the revelation that he used to have a piece of Riddle in his scar, to the nature of the energies that entered his body when he activated the Millennium Puzzle, Heck with the ease that he could now use his brain he might as well reexamine his three years at Hogwarts, you never know what he will discover.

One thing was for sure his life was going to get more interesting.

 **END CHPATER**

 **A/N: (1) Yugi always shouts that when he activates the Puzzle so it must be a password or something.**

 **I hope you guy liked it, please review if you like, know though that flames will be ignored.**

 **Also for pairing I have something in mind, but if you have a suggestion please put it on your review.**

 **See you guys next time.**


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